A Functional Link between Nuclear RNA Decay and Transcriptional Control Mediated by the Polycomb Repressive Complex 2

Summary: Pluripotent embryonic stem cells (ESCs) constitute an essential cellular niche sustained by epigenomic and transcriptional regulation. Any role of post-transcriptional processes remains less explored. Here, we identify a link between nuclear RNA levels, regulated by the poly(A) RNA exosome targeting (PAXT) connection, and transcriptional control by the polycomb repressive complex 2 (PRC2). Knockout of the PAXT component ZFC3H1 impairs mouse ESC differentiation. In addition to the upregulation of bona fide PAXT substrates, Zfc3h1−/− cells abnormally express developmental genes usually repressed by PRC2. Such de-repression is paralleled by decreased PRC2 binding to chromatin and low PRC2-directed H3K27 methylation. PRC2 complex stability is compromised in Zfc3h1−/− cells with elevated levels of unspecific RNA bound to PRC2 components. We propose that excess RNA hampers PRC2 function through its sequestration from DNA. Our results highlight the importance of balancing nuclear RNA levels and demonstrate the capacity of bulk RNA to regulate chromatin-associated proteins. : ZFC3H1 targets pA+ RNA for decay by the nuclear RNA exosome. Garland et al. report a disruptive relationship between excess RNA and PRC2 upon depletion of ZFC3H1 in mouse ESCs. In such conditions, RNA is bound by PRC2 components, which show reduced binding to chromatin and fellow PRC2 proteins. Keywords: nuclear RNA decay, RNA exosome, PRC2, PAXT, chromatin, H3K27 methylation, stem cell regulation